Real-time search of all bacterial and viral genomic data [article]

Phelim Bradley, Henk den Bakker, Eduardo Rocha, Gil McVean, Zamin Iqbal
2017 bioRxiv   pre-print
Genome sequencing of pathogens is now ubiquitous in microbiology, and the sequence archives are effectively no longer searchable for arbitrary sequences. Furthermore, the exponential increase of these archives is likely to be further spurred by automated diagnostics. To unlock their use for scientific research and real-time surveillance we have combined knowledge about bacterial genetic variation with ideas used in web-search, to build a DNA search engine for microbial data that can grow
more » ... ntally. We indexed the complete global corpus of bacterial and viral whole genome sequence data (447,833 genomes), using four orders of magnitude less storage than previous methods. The method allows future scaling to millions of genomes. This renders the global archive accessible to sequence search, which we demonstrate with three applications: ultra-fast search for resistance genes MCR1-3, analysis of host-range for 2827 plasmids, and quantification of the rise of antibiotic resistance prevalence in the sequence archives.
doi:10.1101/234955 fatcat:p6wjflaikzhczlsjs2nro4sh2i